research proposal molecular biology

PhD projects 2024

Many of our PIs are recruiting doctoral candidates in this year's application round. Below you can find their project proposals or research descriptions. Get inspired by these to draft the research proposal for your application. Your research proposal should be longer than the summary provided here (approximately 2-3 pages) and should show some of your own input, including a title, a short background of the topic, a research question, proposed methods and references. Moreover, we encourage you to explain how you plan to include both sides of the experimental-theoretical spectrum in your project. For instance, how could laboratory experiments help support the conclusions of your bioinformatics project? Which bioinformatics tools do you plan to include in your wet laboratory project?  

[NEW] - Co-evolution of transposable element activity and host genome

[NEW] - Understanding the Distribution of Mutations along Genomes

[NEW] - Chromatin regulation in stem cells and development

[NEW] - Molecular mechanisms of genome transcription regulation & dysregulation

[NEW] - Investigating Antisense Oligonucleotide (ASO) Treatments for Neurodegenerative Diseases

[NEW] - Transcriptional condensates

[NEW] - Computational systems medicine and disease control

[NEW] - Comparative Analysis of DNA Methylome Conservation Across Species

[NEW] - Genome Regulation Department

[NEW] - Synthetic biology of long-range gene regulation

[NEW] - lncRNAs in 3D – dissecting the gene regulatory function of long non-coding RNAs 

[NEW] - Evolution of primate transcription factor genes

Mathematical modelling of cis-regulatory landscapes

[NEW] - Epigenetic mechanisms controlling cell fate decisions during the early stage of liver, pancreas and biliary tree development

[NEW] - Transcriptional Regulation Group

[NEW] - Molecular mechanisms of bacterial immunity

Browse Course Material

Course info, instructors.

• Prof. Christopher Burge
• Prof. David Sabatini
• Dr. Marilee Ogren-Balkema
• Dr. Alice Rushforth

Departments

As taught in.

• Biotechnology
• Molecular Biology

Learning Resource Types

Experimental molecular biology: biotechnology ii, scientific comm..

This course includes significant instruction in scientific communications. During the term, Dr. Marilee Ogren-Balkema presents ten lectures on a range of reading, presentation and writing topics.

Background reading

Gopen, George D., and Judith A. Swan. “ The Science of Scientific Writing .” The American Scientist 78 (1990): 550-558.

Lectures on Scientific Communications

1: Basic Scientific Communication ( PDF )

2: How to Review the Literature ( PDF )

3: How To Write a Research Proposal ( PDF )

4: Preparing Effective Oral Presentations ( PDF )

5: How to Write a Mini Literature Review ( PDF )

6: How to Write a Research Paper I: Illustrations ( PDF - 1.2 MB )

7: How to Write a Research Paper II: Results Section ( PDF )

8: How to Write a Research Paper III: Methods Section ( PDF )

9: How to Write a Research Paper IV: Introduction and Discussion ( PDF )

10: How to Write a Research Paper V: Title and Abstract ( PDF )

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Department of Biological Sciences

Examples of Undergraduate Research Projects

Fall 2021 projects, previous projects.

MCDB 196A & 196B: Proposal Guidelines

• Proposals should be 1 – 2 pages, typed with 1-inch margins, single-spaced, and 11-pt Arial font
• Title of proposed project
• Student name, UID, and email address (same one on file with the Registrar)
• Faculty research mentor’s full name, department, and email address
• The proposal should be written in your own words, reflecting your understanding of the project. If you utilize materials written by someone else, such as sections of a grant proposal or research article, make sure you cite them appropriately (include in-text citations plus a bibliography). It is a form of academic dishonesty to turn in material written by someone else without giving them proper credit.
• The intent in writing a research project proposal is to convince a review panel such as the undergraduate curriculum committee that the topic and approach are sound and have a clear relationship to previous work in the same field. Students should spend considerable time thinking about their projects, discussing their projects with their research mentors, and producing multiple drafts of the proposal since the quality of this document influences whether or not the application is approved.
• The proposed project should be appropriate in scope for a 20-week project (10 weeks in 196A plus 10 weeks in 196B) and reflect accomplishments expected by both student and faculty advisor.
• A proposal should begin with a problem statement – a clear description of the larger problem within which the research project is situated.
• A description of the project should follow. This should include a rationale for the project that incorporates existing bodies of literature (published works) that will set the project into context, showing how the proposed work builds upon previous studies. This discussion should set the stage for the hypothesis(es) to be tested. The description should incorporate specific aims explaining what you plan to accomplish and how. This section should include a succinct account of methods that will be used to generate data (how will the data be collected and subsequently analyzed?) as well as a justification for why this approach is appropriate (how does it address your hypothesis or address the research question?).
• The proposal must make clear the precise role that the student will play in the lab , including how much and what part of the data collection will be completed.
• The project should reasonably fit the research and writing components within a two-quarter framework imposed by 196A and 196B and require no less than 12 hours per week in the lab. The faculty advisor should provide an estimate of approximately how many hours per week (for the duration of one quarter) the proposed project is expected to involve. That estimate should be included in the project proposal.
• Append the project proposal to the undergraduate research application & acknowledgement form , MCD BIO 196A contract signed by faculty advisor, faculty mentor agreement with signatures from both student and faculty advisor, and submit materials to the online application form.
• Project proposals will be reviewed by departmental curriculum committee. Students will be informed of their decision within 2-3 weeks of submitting application.

NOTE: If you are submitting an MCD BIO 198A (Departmental Honors) contact to be taken along with 180A, please follow the proposal guidelines for a 198A project:  https://www.mcdb.ucla.edu/mcdb-198a-d-proposals/ .  Your proposal will be for a three-quarter project, instead of a two-quarter project.

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Department of Molecular and Cell Biology

Genetics and Genomics

Formal “qualification” for the Ph.D. degree takes place by passing the Dissertation Proposal, a tripartite examination focused upon the student’s dissertation research plans. This exam should be taken at a point at which the student has completed most course work and has research well underway. The student should aim to complete this exam by the end of the third year of graduate study. The three parts of the exam, each of which will be evaluated separately by the full Advisory Committee are:

I. A written proposal II. A seminar presentation on the proposal III. A closed-door question and answer session with faculty

A student who demonstrates acceptable performance on all three parts of the examination, evidenced by a majority vote of the full Advisory Committee to pass on all three sections, “qualifies” for the Ph.D. degree, and continues on that track of study. A student who does not make adequate progress, evaluated by a majority vote of the Committee, may be asked by the Committee to repeat any sections of the examination to achieve a full pass. In cases of inadequate performance on the examination, the Committee may also recommend transfer to one of the Master’s of Science programs.

I. GUIDELINES FOR WRITTEN PROPOSAL PREPARATION

(For Genetics and Genomics doctoral scholars in MCB)

The written proposal has a ten page limit ( excluding references) and the following suggested sections. All figures, tables, charts, and diagrams are included in this 10-page limit. This format is based on current grant submission formats for most federal agencies, which range from 4-12 pages total, preparing the student for succinct presentation and defense of their scientific premise.

You must submit this Proposal two calendar weeks (10 business days) before the scheduled examination to each of your committee members. The thesis advisor may read and make general comments on this document prior to submission, but may not edit it. For some guidelines on writing, Helpful Hints on Scientific Writing.

Cover page: This is not included within the 10-page limitation.

It will include: Title, date of submission, date of scheduled exam, student name, committee members’ names and affiliations.

I. Significance. What are the broad implications of the research that you propose? What is its importance? The significance section should “funnel” consideration from the global to the specific project at hand. One warning: everything you mention in this section is fair game for questioning. Keep focused on the issues you identify as really important. (1/2 – one page)

II. Specific Aims/Goals. Make use of numbered, concise statements of hypotheses/questions. This will immediately focus the reader on precisely what you will be doing, and place the background in context. Keep in mind that this does not have to reflect historical chronology, but rather should present a series of logical steps. (1/2 -one page)

Sections I-II is the total content of Page 1 and cannot exceed one page.

Pages 2-10 Consist of the Following Sections:

III. Background and Preliminary Data. Provide a brief synopsis of the relevant background the reader needs to interpret your proposed research. (2 pages or less) This should not be an exhaustive literature review, but rather should highlight the background needed to place the area of research into context to understand your experimental hypotheses and approaches.

Keep in mind not all members of your committee are in the same area of research; it is critical to explain why the system/question/approaches proposed are interesting, important, and feasible.

In the preliminary data component of this section, a brief presentation of the data collected by the student in support of the approach and aims should be included. Note that considerable variation in the extent of data among students is expected, but only include data relevant to the proposal.

IV. Approach. This section is the bulk of the proposal (4-5 pages). It is a good idea to have a subsection for each hypothesis/question posed in each specific aim. In this section, you are tasked with defending why you should continue for the next 2-4 years on your project. In other words, convince your readers that this work is worthwhile, feasible and will contribute to the field.

Include the following subsections under each aim in the approach section:

A. Rationale . This is a statement of the logic behind your experiment. Include in this section any thinking that went into your hypothesis, any synthesis you might have made.

B. Experimental Plan. Include in this section the strategy you plan to use to address the hypothesis, as well as information about procedures and protocols in general terms. Your committee is more interested in the logic than in the details – reference common procedures. Focus on those aspects that are conceptual rather than technical, but be aware of any limitations of the methodology you select.

C. Interpretations and Alternative Approaches. Make sure you interpret results critically. Showing alternative meanings indicate that you have thought the problem through and are able to meet future challenges. Call attention to potential difficulties you may encounter with each approach. Propose alternatives that would circumvent possible limitations. Committee members will be aware of possible problems; convince them you can handle such circumstances.

For example:

Specific Aim 1: To…

1.A. Rationale – why do this? 1.B. Experimental Plan – how will I do this? 1.C. Interpretations and alternative approaches – what will it mean if I see X or Y? If it does not work because of the following reason…I will perform….to overcome this problem

IV. Timeline and Impact.

In this section, briefly lay out your timeline of experiments for the remainder of your thesis, including anticipated milestones such as publication submissions, conference presentations, and other seminar opportunities. Do not include courses, teaching and other duties not directly relevant to the work.

The impact statement should summarize (2-4 sentences total) what your body of work would contribute to the field, highlighting the advances it makes over existing knowledge.

II. SEMINAR PRESENTATION of PROPOSAL (see Presentation Skills )

Iii. closed door exam.

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Undergraduate Chemical and Physical Biology (CPB) Research and Thesis

Research and thesis.

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A senior thesis is a year-long research for credit course worth 8 credits and is letter graded. Students must identify a faculty sponsor that is willing to host and mentor them latest by the end of Spring semester of Junior year (students may decide to start earlier) since the thesis proposal is due mid-July before senior year. Faculty sponsors must be a Harvard faculty or an affiliate of Harvard. Once your proposal is accepted, you may enroll in MCB/CPB 99AB. Students enrolled in 99AB are expected to work ~15 hours/week during term time. Research mentors are expected to provide training on both the science and writing. The undergraduate office will provide supplemental support by hosting a number of workshops and exercises aimed at improving the quality of presentation and writing.

A full list of all MCB and CPB undergraduate theses is available here.

CPB concentrators are encouraged to do research in any area of the life sciences of interest. Many labs on the Cambridge campus as well as labs at Harvard Medical School or affiliated hospitals host undergraduate researchers. Talk to the ADUS, Dominic Mao ,, Concentration Advisor Monique Brewster , or to the Co-Head-Tutors, about how to find a lab that matches your interests. You may also contact the undergraduate science research advisor, Kate Penner

Useful links:

• How to get involved with research.
• Open undergraduate research positions
• URAF Independent Research Fellowships

Undergraduate Research

Lab research.

Biochemistry and Molecular Biology (BMB) majors can earn academic credits and gain important real-life experience doing independent study (IS) research. A typical campus research lab has a Principal Investigator (PI), a professor who writes the grant proposals to obtain funding to support the lab, supervises the research, and supervises the writing of research manuscripts for publication. The lab members may include postdoctoral fellows (postdocs) who are recent PhD graduates, PhD or MS graduate students, other undergraduate students, and technicians. All work closely together on a particular research problem, with each member pursuing an agreed-upon, but independent, role in the project. Students can join a research team at any point during their undergraduate career.

No, all BMB majors who have a GPA of 3.0 or higher are eligible to participate in IS research.

No, you will most likely be added to one of the ongoing projects where you will be shown the basic techniques and allowed to develop lab skills, and you will start on a portion of a project that is feasible for an agreed-upon number of hours per week in a semester.

BMB majors are generally expected to have a GPA of 3.0 or above. Some faculty members may want you to have taken certain courses before joining their lab.

Credits range from one to six and are based on an agreement between you and the faculty member whose lab you will join. Typically, one credit is equivalent to approximately three to four hours of work per week.

IS sections are not structured in the same way as a lab or lecture course. Grading expectations should be described by the faculty member upon joining the lab. Often the expectations include attending regular lab meetings, presenting at lab meetings, sharing regular written summaries of your findings, and completing a final written report or presentation of a poster.

No, BMB majors have a wide variety of labs to choose from outside of the BMB department. The field of biochemistry and molecular biology is cross-disciplinary by its very nature, and there are many labs across campus conducting research that is very relevant to BMB majors.

Finding a Research Lab

We recommend visiting the  Office of Undergraduate Research & Studies (OURS)  for help finding undergraduate research opportunities on and off campus. OURS has peer advisors who will help you identify labs and develop your approach to faculty.  Check out their YouTube video to learn more ! OURS has also created a short  Research Readiness Moodle course  that provides information about getting involved in research and guides you on ways to turn your interests into research projects.

Identify  several  faculty with whom you may want to work.

Contact individual faculty members by email.

• Include your major, class year, career goals and interests, and express why you are interested in their lab.
• Provide a resume.  The CNS Career and Professional Development Center  holds resume workshops and has staff and peer advisors who can work with you on your resume.
• Request an appointment to discuss a possible research project. Provide your general availability over a two-week time frame.
• Allow adequate time for the faculty to respond. If necessary, send a friendly follow-up email to the PI. Be persistent and patient.

Arrange to meet with each PI, and be prepared!

• Learn the basic information about the PI’s research from their webpage.
• Prepare questions to ask the PI about the research, and specifically inquire about projects available for undergraduates.
• Think about how much time you have available to work in the lab each semester, taking into account your other time commitments when you consider the number of academic credits you want to earn each semester.

Enrolling in an Independent Study

Enrollment in IS sections is by instructor consent. As with other courses, students can only be enrolled in IS sections before the end of Add/Drop. Consider volunteering in the lab during your first semester if you are unable to find a research lab before the Add/Drop deadline.

Obtain the appropriate form:

• For non-Honors IS, students should complete the  BMB Independent Study Form  online. Students can enroll in a Biochem IS course regardless of which department their PI is from.
• For Honors IS, students who are members of CHC should complete an Honors Independent Research Form through  CHC PATHS . Proposal requirements can be found by clicking on the "ISH Proposal Creation" link on your PATHS dashboard.

Both of these forms require detailed information on the work you will be doing in the lab. Please work with your PI or your graduate student supervisor to get all of the necessary information before submitting your form.

IS courses taken at the 300- and 400-level will count toward  the required 8 credits of advanced electives . These form submissions will be carefully reviewed to ensure that the work you are doing in the lab is rigorous enough to count as an advanced elective.

BMB majors who are members of CHC are encouraged to do their Departmental Honors Thesis work in BMB labs, if possible (Biochem 499Y and 499T). However, in the case where an Honors student pursues work in a lab outside BMB, they must get approval from  one of the BMB Honors Program Directors  and have a BMB faculty member serving on the thesis committee. The Honors Program Director must sign their approval of the Honors Research Contract and accompanying preliminary proposal before enrollment in Biochem 499Y/T. See the CHC webpage describing the requirements for the  individually contracted Honors Thesis proposal .

Questions about IS enrollment can be directed to  @email .

Tips for Working in a Lab

You're in a research lab! Now what?  Learn how to make the most out of your undergraduate lab experience .

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• Published: 16 May 2024

The LexA–RecA* structure reveals a cryptic lock-and-key mechanism for SOS activation

• Michael B. Cory   ORCID: orcid.org/0000-0002-2509-2939 1 ,
• Allen Li   ORCID: orcid.org/0000-0003-4519-450X 2 ,
• Christina M. Hurley   ORCID: orcid.org/0000-0002-8821-7233 1 ,
• Peter J. Carman 1 ,
• Ruth A. Pumroy 3 ,
• Zachary M. Hostetler 4 ,
• Ryann M. Perez 2 ,
• Yarra Venkatesh 2 ,
• Xinning Li 2 ,
• Kushol Gupta   ORCID: orcid.org/0000-0002-7006-2667 3 ,
• E. James Petersson   ORCID: orcid.org/0000-0003-3854-9210 2 , 3 &
• Rahul M. Kohli   ORCID: orcid.org/0000-0002-7689-5678 3 , 4  

Nature Structural & Molecular Biology ( 2024 ) Cite this article

705 Accesses

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• Cell signalling
• DNA damage and repair
• Electron microscopy
• Enzyme mechanisms

The bacterial SOS response plays a key role in adaptation to DNA damage, including genomic stress caused by antibiotics. SOS induction begins when activated RecA*, an oligomeric nucleoprotein filament that forms on single-stranded DNA, binds to and stimulates autoproteolysis of the repressor LexA. Here, we present the structure of the complete Escherichia coli SOS signal complex, constituting full-length LexA bound to RecA*. We uncover an extensive interface unexpectedly including the LexA DNA-binding domain, providing a new molecular rationale for ordered SOS gene induction. We further find that the interface involves three RecA subunits, with a single residue in the central engaged subunit acting as a molecular key, inserting into an allosteric binding pocket to induce LexA cleavage. Given the pro-mutagenic nature of SOS activation, our structural and mechanistic insights provide a foundation for developing new therapeutics to slow the evolution of antibiotic resistance.

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Plasmid targeting and destruction by the DdmDE bacterial defence system

Structural mechanism of angiogenin activation by the ribosome.

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Data availability.

The cryo-EM maps and associated atomic model for this study have been deposited to the Electron Microscopy Data Bank (EMD- 41579 ) and Protein Data Bank ( 8TRG ). The earlier maps and model used as a comparison in this work are available on the Electron Microscopy Data Bank (EMD- 34152 ) or the Protein Data Bank ( 1JHE , 3JSP , 8GMS ). Source data are provided with this paper. All other data necessary to evaluate the claims in the paper is present in the text or Supplementary Information . Plasmids for LexA or RecA variants are available upon request.

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Acknowledgements

This work was supported by the National Institutes of Health (grant no. R01-GM127593 to R.M.K. and E.J.P.). R.M.K. holds an Investigators in the Pathogenesis of Infectious Disease Award from the Burroughs Wellcome Fund. The National Institutes of Health also provided training grants (grant nos. T32-AI141393 for M.B.C. and T32-GM133398 for C.M.H. and R.M.P.) and mass spectrometry instrumentation support (grant no. S10-OD030460). Structural data collection was performed with the help of the Institute of Structural Biology, the Electron Microscopy Resource Laboratory and the Beckman Center for Cryo-EM at the University of Pennsylvania (RRID: SCR_022375). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

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Contributions

M.B.C., E.J.P. and R.M.K. conceived of the experiments. M.B.C. designed the overall experimental plan. M.B.C., A.L., C.M.H., Z.M.H. and Y.V. designed and executed biochemical experiments. M.B.C., A.L., P.J.C., R.A.P. and K.G. designed structural biology experiments, collected associated data and performed analysis. R.M.P. and X.L. performed computational modeling experiments. M.B.C., E.J.P. and R.M.K. wrote the manuscript. All authors were involved in editing and reviewing.

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Correspondence to E. James Petersson or Rahul M. Kohli .

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Extended data

Extended data fig. 1 cryo-em analysis pipeline..

The flow of data from the collected and filtered micrographs through the final local refinement is shown. Each labeled step includes relevant information for the partitioning of data at each junction. For each refinement and reconstruction step, the FSC curve generated by CryoSPARC is shown.

Extended Data Fig. 2 Characteristics of the EM density and model.

a ) Final sharpened map colored by the estimated local resolution using Relion. The entire complex is shown at top, with the relevant sub-complex components at the bottom with RecA* and LexA labeled and colored relative to grayed out other components. b ) Orientation distribution of the final particle stack as determined by cryoEF. Orientation efficiency, Eod is given below. c ) Closeup of the ATP binding pocket at the interface of two RecA protomers within the filament, showing the coordinated Mg 2+ ion in green. Density from the two independent half maps and the corresponding full map at a contour level of 0.203 and 0.172 respectively shown in mesh. d ) Closeup of the bound ssDNA within the filament. Density from the two independent half maps and the corresponding full map at a contour level of 0.203 and 0.172 respectively shown in mesh.

Extended Data Fig. 3 Comparison to prior models.

a ) Global comparison of this current model of full-length LexA bound to RecA* (8TRG, blue and pink) to prior published model of a RecA* dimer bound to the CTD-only LexA (8GMS, gold and sea green). Global RMSD is between Cα atoms of residues present in both models, RMSD of the L2 pocket is all-atom of the residues shown by sticks. b ) Overlay of the current model of the SOS complex with native, full-length LexA into the cryoEM density from Gao et al (Ref. 32 ). The displayed density is that derived from 8GMS, and is colored to match the model colors from A (LexA in gold, RecA* in sea green), including the density from a second LexA CTD (dark orange). The ribbon structures show our fit model, colored accordingly (8TRG, blue and pink). The overlay demonstrates that full-length LexA containing the NTD is not compatible with the symmetrically decorated filament previously studied with CTD-only LexA. c ) Molecular dynamics was performed to build potential poses for the missing NTD from the unbound LexA subunit. Five distinctive poses were selected in this overlay, represented by different colors in ribbons, with the cryo-EM density-derived model shown as a surface.

Extended Data Fig. 4 Discrimination between operator-bound LexA and free LexA by RecA*.

a ) SDS-PAGE gel of autoproteolysis of fluorescent LexA-CF variant at pH 7.5 in the absence of operator or in the presence of either 20 bp or 40 bp consensus operator (single replicate). b ) Fluorescence anisotropy of LexA-δ with various in vitro binding partners. Each data point represents a single replicate. The various contributing species to the observed anisotropic signal are given to the right. c ) Equilibrium endpoint anisotropy titration of either Ec or Mtb LexA with FAM-labeled 40-mer consensus operator. Data shows a single replicate and the solid line is a fit to a quadratic equation, using a fixed [operator] of 1 nM. d ) SDS-PAGE analysis of RecA*-dependent cleavage of E. coli LexA with either an Ec or Mtb inter-domain linker when incubated with consensus operator (single replicate). e ) Structural overlay of our modeled SOS complex (8TRG, blue and pink) with the crystal structure of the DNA-bound LexA dimer (3JSP, yellow). Steric clashes are colored in red. Lower left panel shows a close-up view of one of the modeled bound LexA NTD alongside the corresponding DNA-bound NTD, demonstrating the distinctive orientations of the NTDs in the two different structures. The relative numbering of each alpha helix in the NTD is numbered according to the topological diagram on the left side of the panel.

Source data

Extended data fig. 5 alkaline autoproteolysis rates of each tested lexa variant..

Data were fit to a single exponential decay (solid line) with 95% confidence intervals shown (shaded region). The best-fit value for the decay rate is shown on each graph. Data represents the mean from three replicates, with error bars denoting standard deviation.

Extended Data Fig. 6 Analysis of potential charge-charge interactions between RecA* and LexA.

a–c ) Three different sections within the interaction interface that provide potential charge-charge interactions. Each of the RecA protomers within the three consecutive RecA units providing a majority of the contacts are highlighted and labeled in shades of pink to purple. The bound LexA monomer is shown in blue. Insets highlight the distances between interacting residues in green and show the sharpened map density as a wire-mesh surface. The panels highlight A) the ‘CTD Patch’ of interaction residues between RecA* and LexA. B) the ‘L2 Stabilizing Patch’ interaction residues, and C) the ‘NTD Patch’ interaction residues. d ) Top: Representative SDS-PAGE analysis of RecA*-dependent cleavage of CTD patch residues in isolation or in combination. Bottom: Quantified LexA cleavage of CTD mutants expressed as a percentage of WT LexA rate (normalized to 100% shown by the dotted line; derived from n = 10 independent WT cleavage replicates). Each bar represents the mean from replicates (grey circles; n = 7 independent cleavage experiments for single mutants and n = 4 for QM) and error bars denote standard deviation. Below the graph, the posterior likelihoods of being either less than WT or greater than QM CTD are given via pairwise Bayesian comparisons of sample means, assuming unequal variance between samples. e ) Top: Representative SDS-PAGE analysis of RecA*-dependent cleavage of L2-stabilizing patch residues. Bottom: Quantified LexA cleavage of L2-stabilizing mutants in isolation or in combination, expressed as a percentage of WT LexA rate (normalized to 100% shown by the dotted line; derived from n = 10 independent WT cleavage replicates). Each bar represents the mean from replicates (grey circles; n = 7 independent cleavage experiments for single mutants and n = 3 for QM) and error bars denote standard deviation. Below the graph, the posterior likelihoods of being either less than WT or greater than DM L2 are given via pairwise Bayesian comparisons of sample means, assuming unequal variance between samples.

Extended Data Fig. 7 Allosteric binding pocket on LexA and species variation.

a ) Surface (left) and cartoon (right) representations of the SOS complex model, as shown in Fig. 2 . RecA F203 (pink) is bound to LexA (blue) within the hydrophobic pocket formed by the highlighted LexA residues (purple). The map density is shown on the right as a mesh surface. b ) Sequence alignment of LexA and RecA proteins from select different species, showing the LexA hydrophobic pocket residues (left) and a subsection of the RecA L2 loop (right). F203 is highlighted in pink.

Extended Data Fig. 8 Biochemical analysis of RecA3x mutant filamentation and LexA binding.

a ) RecA3x mutant filamentation expressed as a percentage of RecA3x WT anisotropy (normalized to 100% shown by the dotted line; derived from n = 3 independent RecA3x filamentation experiments) in the FAM-ssDNA binding assay. Data show the means of three replicates, with error bars denoting standard deviation. b ) RecA3x mutant binding to LexA-δ expressed as a percentage of RecA3x WT anisotropy (normalized to 100% shown by the dotted line; derived from n = 3 independent RecA3x binding experiments) in the LexA binding assay. Data show the means of three replicates, with error bars denoting standard deviation. All samples had >0.999 posterior likelihood (via pairwise Bayesian comparisons of sample means, assuming unequal variance between samples) of being less than WT, and the posterior likelihoods of each successive mutant being less than the prior mutant is shown.

Extended Data Fig. 9 LexA and RecA constructs.

Shown is an SDS-PAGE gel including various LexA constructs evaluated in this study with the molecular weights of the ladder labeled at left (single replicate).

Supplementary information

Reporting summary, source data fig. 3.

Unprocessed SDS–PAGE gels with labels.

Source Data Fig. 4

Statistical source data.

Source Data Fig. 5

Source data fig. 6, source data extended data fig. 4.

Gels for Extended Data Fig. 4.

Source Data Extended Data Fig. 5

Source data extended data fig. 6, source data extended data fig. 8, source data extended data fig. 9, rights and permissions.

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Cory, M.B., Li, A., Hurley, C.M. et al. The LexA–RecA* structure reveals a cryptic lock-and-key mechanism for SOS activation. Nat Struct Mol Biol (2024). https://doi.org/10.1038/s41594-024-01317-3

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Received : 14 September 2023

Accepted : 15 April 2024

Published : 16 May 2024

DOI : https://doi.org/10.1038/s41594-024-01317-3

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