What limits rubisco function? Is it the chemical mechanism? Evolution? In an updated pre-print
@prywes
et. al explore this question by assaying >99% of single amino acid mutants in Form II rubisco (1/7)
🚨 New pre-print! We engineered catalytically inactive and improved
#Cas13
effectors for efficient post-transcriptional regulation of genes in bacteria and human cells. 1/5
Former Amgen scholar
@caroguerrero522
enjoyed her summer in the Savage lab so much she decided to come back for more. Excited to welcome this Savage Cat back to the lab as a grad student!
Years in the making - a peroxidase-encapsulating nanocompartment helps M. TB survive oxidative stress in acidic environments including in hosts! Amazing collaboration between Katie Lien,
@Nichols_NTA
and Caleb CA,
#SavageCats
and Stanley Lab.
New work out from Savage Cats! “CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification” congrats to Ben, Christoff, Harneet, Kian, Rayka et al!!!!
Please RT! We’re looking to hire a postdoc interested in CRISPR biochemistry with a focus on diagnostics! Interested candidates can DM this account or email savage
@berkeley
.edu with a CV & cover letter.
We’ve had much cause to celebrate lately, including bidding a bittersweet farewell to Eli Dugan, our amazing lab manager who is starting his PhD at
@UCSF
Tetrad in the Fall! 🥳 Also 👏🏾 to our commander-in-chief
#Dave
(
@dfsavage
) for TEN YEARS at
@UCBerkeley
😳😮💨🔟
Big congrats to Luke and Benz on the culmination of untold hours scrutinizing csos2! Now we finally understand how this strange disordered repeat protein brings rubisco to the carboxysome.
#savagecats
#upwardsandonwards
We are looking to hire a Science Research Associate to work with us at the interface of protein design + CRISPR/Cas + applied gene editing! Please share broadly!
Rubisco is, after all, an enzyme, so we wanted to biochemically characterize each mutation. By repeating the assay over CO2 titration, key biochemical parameters (e.g. Vmax, Kc) are estimated for each mutant! (5/7)
Huge congrats to our very own Rob Nichols
@Nichols_NTA
- just posted his paper on the discovery and characterization of a whole new sulfur-metabolizing branch of the bacterial nanocompartment family - "family 2 encapsulins." Rewarding collabo with
@bjlafrance
and
@NogalesLab
So happy to see our pre-print online!! We discovered an characterized a new prokaryotic organelle - a novel family of encapsulins! With the help of
@bjlafrance
and the
@NogalesLab
we determined the structure of the compartment to 2.2 Angstrom resolution!!
BREAKING NEWS:
The 2020
#NobelPrize
in Chemistry has been awarded to Emmanuelle Charpentier and Jennifer A. Doudna “for the development of a method for genome editing.”
HHMI News: We are proud to announce our 33 new
#HHMIInvestigators
. These individuals have the potential to make transformative discoveries over time and we look forward to seeing where their ideas lead them.
It’s been a big year for E. coli - she graduated from heterotrophy school and has been learning a lot of new metabolisms! Congrats to Bar-Even lab on the culmination of many years of work!!
Every day in the Savage Lab we ask ourselves, "what's new with
#carboxysome
engineering?" If you find yourself new to this line of thinking, fear not! Our own
@JuliaBorden
has authored a
#review
on the topic for your reading pleasure! 👇
#synbiothoughts
But wait, there's more! New work by Turnšek et al. identifies key residues that drive this assembly, shows the effects of mutation in vivo, and probes the biochemistry in vitro with reconstituted carboxysomes!
In the first preprint of the weekend,
@loltrogge
et al. find that the size of α-carboxysomes is strongly specified by CsoS2 and, in particular, the relative abundance of M- and C-type peptide repeats. ⬇️
Small changes in sequence can have big consequences in function, and not only negatively! We hope that this data is useful to other enzyme engineers and that this result expands our view of what is possible with even small changes. (7/7)
The year of the encapsulin CONTINUES with our new paper w/
@bjlafrance
, Caleb Cassidy-Amstutz, and
@NogalesLab
. We show that a nanocompartment shell binds flavin, suggesting it could participate in redox chemistry... This one is HOT- call it Thermatoga!
To address this,
@prywes
et al developed an assay to estimate the fitness of 99% of single mutations in a high-throughput E. coli screen. E. coli growth rate is linked to enzyme behavior! (3/7)
Things our beloved postdoc
@cblikstad
will miss about California, in ascending order:
- the CA sea and sun
- working with CArboxysomes
- her wonderful labmates, the Savage CAts
Please join us in wishing Cissi well as she starts her own group in
@chem_angstrom
at
@uppsalauni
! 🧑🔬
Exciting new work by our labmate Luke Oltrogge et alia: dissection of the mechanism of csos2-mediated recruitment of Rubisco into the alpha carboxysome.
As the entry-point for nearly all CO2 to the biosphere, rubisco is arguably one of the most important enzymes. Yet, Rubisco catalysis is slow. While there are 100s of biochemical measurements, our understanding of catalysis is limited by low-throughput in vitro assays (2/7)
Several single AA mutations increased the CO2 affinity! Given sequence divergence and different oligomeric states of Form I & II, we were surprised to find single muts led to CO2 affinity outside of the range of Form II & at the edge of the distribution of plants and algae (6/7)
Big congrats to our friends in the Milo Lab
@WeizmannScience
on publishing this huge achievement: "Conversion of Escherichia coli to Generate All Biomass Carbon from CO2"
This assay neatly identified known structural, functional, and evolutionary effects, confirming the robustness of the screen. For example, key residues in Loop 6 and the active site, are mutation-intolerant (4/7)
Our talented technician, Emily Meier (
@emileedle_
), is off to
@HopkinsCMDB
for her PhD! Emily has been a wonderful and valuable member of the lab and the diagnostics team, and we’re excited for her adventures in Baltimore! 👩🔬🧬✌️
Everyone should read this fabulous paper from Manajit Hayer-Hartl’s lab. We saw her speak about it recently and it is phenomenal work that explains a lot about beta carboxysome formation.
Wowww, carboxysomes? 😯 Carbonic anhydrases?? 😮💨 RUBISCO??? 🤯 This preprint from Savage Cat
@cblikstad
(now Group Leader at
@UU_University
) has it all!! Check out the thread below for an explainer. Congrats Cissi et alia! 🦠
Happy to share that our work on how carbonic anhydrase encapsulates into α-carboxysomes is now on Biorxiv. Tl;dr: We discovered a carbonic anhydrase-Rubisco supercomplex and solved a sub 2 Å cryoEM structure.
@SavageCatsOnly
@berkeleyMCB
1/
🆒🆕 Super cool work by
@patrick_pausch
et. al. on the characterization of a new CRISPR protein, CasΦ, that can cut dsDNA despite being ~half the size of Cas9! 🧬✂️
Very excited to share my first postdoc paper. We experimentally characterized the hypercompact CRISPR-CasΦ system (type V-J). At half the size of Cas9, CasΦ is still able to cut dsDNA. Great collaboration with
@themicrobeguy
,
@ScienceMagazine
(1/6)
Savage cats do Halloween. Costumes include: unicorn pusheen, triceratops,
@scotusginsburg
does science, and quite possibly the best Mario and Luigi you will ever see IRL!!! 🦄🐱🦖👩⚖️👨🏻🔧👨🏻🔧
Whew, we've got a double-whammy preprint drop for you to peruse this weekend!
@flamholz
& Eli et al, along with Renee
@Caltech
GPS &
@Nichols_NTA
has a step-by-step guide on how to develop a superpower ⁽ᶦⁿ ᵇᵃᶜᵗᵉʳᶦᵃ⁾ 🦠💪⚡️ 1/3
1/ We are excited to take the wraps off Scribe Therapeutics - a molecular engineering company focused on building best-in-class in vivo therapies to permanently treat the underlying cause of disease. Read our launch press release:
Congrats to Rob on a great PhD!!! 🍻🍻Rob set out to answer some of the great mysteries of the prokaryotic nanocompartments (AKA encapsulins) for his dissertation. Turns out there are a bunch of these systems and there are even more questions/ mysteries now!
Pretty
#Savage
perspective out in Biochemistry describing recent work by Manajit Hayer-Hartl's lab showing that liquid-liquid phase separation of rubisco+ccmM underlies the formation of the beta carboxysome. Wise words by
@cblikstad
@flamholz
and Luke
Congratulations to
@flamholz
, Eli,
@cblikstad
and
@MiloLabWIS
collaborators - this paper is the culmination of many years of work, and many decades of collective effort studying bacterial CO2 concentrating mechanisms. So exciting to see it in the world!
Amazing work by
@JoshCofsky
of
@doudna_lab
figuring out how exactly DNA is interrogated by Cas9! If only we had this for all the engineered variants out there… 👀😮💨
New pre-print! While
#CRISPR
-Cas9 searches through the genome, how does it actually "read" DNA sequence information, which is normally hidden within the double helix? We determined structures of Cas9 in the act of DNA interrogation to find out! Thread below 👇 (1/8)
We've updated our white paper, "A protocol for rapid detection of SARS-CoV-2 using CRISPR: SARS-CoV-2 DETECTR." Check it out to learn how our DETECTR platform could be used to detect SARS-CoV-2
#COVID
ー19
#COVID19
#CRISPR
#Diagnostics
#CRISPRDx
👑 Capping off the end of a successful summer CRISPRing plants with
@AmgenFoundation
Scholar Carolina Guerrero! Look out for her next year in a PhD program near you 👀
#amgenscholars
🌱
Back at it with another double preprint drop 📝📝Starring the repetitive, disordered, and “mysterious” scaffold protein CsoS2 and its role in the α-carbozysome. Two (Twitter) threads incoming! 🤩
Today,
@SavageCatsOnly
would like to remind you: quantity =/= quality.
@Choano_Lab
might have this Twitter the rest of the year, but we only need one week 💁♀️💁♂️.
RuBisCO™️: trade name for the worst-tasting yet most abundant rhubarb-flavored cookies on the planet.
Very honored that I have been awarded the
@LSRFdtn
postdoctoral fellowship! I'm really happy to join this community and grateful for my amazing lab
@SavageCatsOnly
and my mentor
@dfsavage
for their continued support!
#SavageWeek
is over! As
@KingLabWOTD
reverts back to its steady-state next week, we'll be honoring the
@SavageCatsOnly
tradition of Mimosa Mondays 🥂 with 96-well-format DIP.
DIP-seq (n.): (alt. "dip-seek") A high-throughput strategy to locate the best dip for group meetings.
LSRF is pleased to announce our 2021 class of awardees! We thank our outstanding team of reviewers and, of course, the organizations and individuals providing the funding for these researchers. Congratulations!
#BasicResearch
,
#LifeScience
,
#PostdocFundin
…
Finally a structure of the cyanobacterial CO2 uptake complex! For those who don't know, cyanos can take up both CO2 and HCO3-, but the CO2 uptake mechanism is complex and mysterious. Amazing contribution to the CCM field. Congrats to
@SchullerJm
@TheKailaLab
@NowaLab
et alia.
Here at
@SavageCatsOnly
we are thrilled to present a review on rubisco. We focused on structure, mechanism, evolution and engineering attempts. We try, and fail, to conclusively answer the question "What exactly is holding this enzyme back?" 1/10
@FPbase
is published in
@naturemethods
! So very thrilled to see what started as a fun side project get released today in one of my favorite journals. Thank you
@rita_strack
for the encouragement.
Just out from
@3rdFloorTom
- a really clear and comprehensive review of recent structures of photosynthetic NADH dehydrogenase-like complexes (NDH-1). Super clear figures and explanation of structure/function relationship for plants/cyanos/algae.
Need a quick primer on
#scicomm
and
#sciencetwitter
? You probably do. Our own
@JuliaBorden
wrote a Toolbox for the latest edition of
@BerkeleySciRev
! Pick your copy up today! 🤙🤓
(We won’t comment on the fact that this account is not on the “suggested people to follow” list)