CRISPR-Mediated Adaptive Immune Systems in Bacteria and Archaea

Sorek, Rotem; Lawrence, C. Martin; Wiedenheft, Blake

doi:10.1146/annurev-biochem-072911-172315

Cited by 601 publications

(500 citation statements)

References 158 publications

(412 reference statements)

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“…In addition, several proteins encoded by pSYSX and pSYSA were markedly down-regulated in DndbC compared with the wild type in both HC and LC conditions (Table III). Among them are CRISPR2 and CRISPR3 (Scholz et al, 2013), which belong to the CRISPR/Cas systems responsible for resistance to horizontal gene transfer, including phage transduction, transformation, and conjugation (Marraffini and Sontheimer, 2008; for review, see Sorek et al, 2013). However, the influence of NdbC deletion on these proteins remains unclear, since the mutant could have experienced problems with plasmid replication connected to the hindrance in cell division.…”

Section: Deletion Of Ndbc Distorts Cell Divisionmentioning

confidence: 99%

Role of Type 2 NAD(P)H Dehydrogenase NdbC in Redox Regulation of Carbon Allocation in Synechocystis

et al. 2017

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H dehydrogenases comprise type 1 (NDH-1) and type 2 (NDH-2s) enzymes. Even though the NDH-1 complex is a wellcharacterized protein complex in the thylakoid membrane of Synechocystis sp. PCC 6803 (hereafter Synechocystis), the exact roles of different NDH-2s remain poorly understood. To elucidate this question, we studied the function of NdbC, one of the three NDH-2s in Synechocystis, by constructing a deletion mutant (DndbC) for a corresponding protein and submitting the mutant to physiological and biochemical characterization as well as to comprehensive proteomics analysis. We demonstrate that the deletion of NdbC, localized to the plasma membrane, affects several metabolic pathways in Synechocystis in autotrophic growth conditions without prominent effects on photosynthesis. Foremost, the deletion of NdbC leads, directly or indirectly, to compromised sugar catabolism, to glycogen accumulation, and to distorted cell division. Deficiencies in several sugar catabolic routes were supported by severe retardation of growth of the DndbC mutant under light-activated heterotrophic growth conditions but not under mixotrophy. Thus, NdbC has a significant function in regulating carbon allocation between storage and the biosynthesis pathways. In addition, the deletion of NdbC increases the amount of cyclic electron transfer, possibly via the NDH-1 2 complex, and decreases the expression of several transporters in ambient CO 2 growth conditions.

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Section: Deletion Of Ndbc Distorts Cell Divisionmentioning

confidence: 99%

Role of Type 2 NAD(P)H Dehydrogenase NdbC in Redox Regulation of Carbon Allocation in Synechocystis

et al. 2017

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“…CRISPRs are transcribed to short RNAs (crRNA) that together with the accompanying CAS proteins form a complex that specifi cally identifi es and degrades invading DNA. CRISPR spacers are acquired during phage infection and serve as a recognition sequence for repeating infection by the same phage (reviewed by Sorek et al, 2013). A survey of CRISPR loci in cyanobacterial genomes revealed their presence in 50 out of 54 analyzed genomes (Shih et al, 2013) and there is no doubt that they are widely distributed among cyanobacteria.…”

Section: Crispr Phage Immunity Systemmentioning

confidence: 99%

Cyanobacterial defense mechanisms against foreign DNA transfer and their impact on genetic engineering

2013

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SUMMARYCyanobacteria display a large diversity of cellular forms ranging from unicellular to complex multicellular fi laments or aggregates. Species in the group present a wide range of metabolic characteristics including the fi xation of atmospheric nitrogen, resistance to extreme environments, production of hydrogen, secondary metabolites and exopolysaccharides. These characteristics led to the growing interest in cyanobacteria across the fi elds of ecology, evolution, cell biology and biotechnology. The number of available cyanobacterial genome sequences has increased considerably in recent years, with more than 140 fully sequenced genomes to date. Genetic engineering of cyanobacteria is widely applied to the model unicellular strains Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942. However the establishment of transformation protocols in many other cyanobacterial strains is challenging. One obstacle to the development of these novel model organisms is that many species have doubling times of 48 h or more, much longer than the bacterial models E. coli or B. subtilis. Furthermore, cyanobacterial defense mechanisms against foreign DNA pose a physical and biochemical barrier to DNA insertion in most strains. Here we review the various barriers to DNA uptake in the context of lateral gene transfer among microbes and the various mechanisms for DNA acquisition within the prokaryotic domain. Understanding the cyanobacterial defense mechanisms is expected to assist in the development and establishment of novel transformation protocols that are specifi cally suitable for this group.

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“…RAMP domains are found in the Cas5, Cas6, Cas7 and Cmr3 families and RAMP-like domains are also found in Cas2 and Cas10. 2,3 However, the ferredoxin-like fold is defined in the SCOP database 4 (and elsewhere) as a babbab or (bab) 2 fold, resulting in a 4 stranded antiparallel b sheet arranged as b 2 b 3 b 1 b 4 . The two helices, present as righthanded crossovers between the b strands, lie on the same face of the b-sheet where they run antiparallel to each other (Fig.…”

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confidence: 99%

Recognition of a pseudo-symmetric RNA tetranucleotide by Csx3, a new member of the CRISPR associated Rossmann fold superfamily

Topuzlu

Lawrence

2016

RNA Biology

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The CRISPR/Cas adaptive immune system shows extreme diversity in the number of CRISPR/Cas types and subtypes, and in the multitude of CRISPR associated protein families of which they are composed. Despite this diversity, the roles of many Cas protein families are now defined with regard to spacer acquisition, crRNA biogenesis, and DNA or RNA surveillance and targeting. However, a number of unclassified CRISPRCas proteins remain. Such proteins have traditionally been designated as CRISPR subtype x (Csx). Here we revisit the structural analysis of one such protein, Csx3, and show that this homodimeric protein utilizes a Rossmann fold for the recognition of an RNA tetranucleotide. Tertiary and quaternary structural similarities of Csx3 to CRISPR/Cas proteins Csx1 and Csa3 are identified and suggest Csx3 is a new member of the CRISPR Associated Rossmann Fold (CARF) superfamily. The structure of the Csx3/RNA complex illustrates one way CARF domain proteins may recognize pseudo-symmetric polynucleotides. Yan et al. recently published "Crystal structures of CRISPRassociated Csx3 reveal a manganese-dependent deadenylation exoribonuclease" in RNA Biology. 1 In this research article the authors present compelling evidence that Csx3 possesses manganese dependent RNase activity and also present crystal structures showing that the manganese and RNA binding sites (Fig. 1A) lie at opposite ends of the Csx3 homodimer. In all, their work represents a significant advance in our understanding of Csx3, providing critical new information relevant to its potential roles in CRISPR/Cas.They also describe the fold of Csx3 (Fig. 1B) as a "ferredoxin-like" fold. At first glance, it is not surprising that Csx3 might also harbor a ferredoxin-like fold. The ferredoxin-like fold (Fig. 1C) is commonly observed in proteins involved in CRISPR-Cas, where it may also be referred to as an RRM (RNA Recognition Motif) or RAMP (Repeat Associated Mysterious Protein) domain. RAMP domains are found in the Cas5, Cas6, Cas7 and Cmr3 families and RAMP-like domains are also found in Cas2 and Cas10. 2,3 However, the ferredoxin-like fold is defined in the SCOP database 4 (and elsewhere) as a babbab or (bab) 2 fold, resulting in a 4 stranded antiparallel b sheet arranged as b 2 b 3 b 1 b 4 . The two helices, present as righthanded crossovers between the b strands, lie on the same face of the b-sheet where they run antiparallel to each other (Fig. 1C). In this context, the Csx3 structure does indeed show a b-sheet flanked on one side by 2 a-helices. But in contrast to the ferredoxin-like fold, Csx3 lacks a 4-stranded antiparallel b sheet, the helices run antiparallel to each other, and the order and connectivity between the b-strands is substantially different (Fig. 1B).The Csx3 fold can, however, be described as a bbababbb(a) structure resulting in a 6-stranded mixed b-sheet in which the b-strands run sequentially across the sheet from b1-b6 (right to left in Fig. 1B). In addition, as a result of right-handed crossover connections provided by helices a1...

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CRISPR-Mediated Adaptive Immune Systems in Bacteria and Archaea

Cited by 601 publications

References 158 publications

Role of Type 2 NAD(P)H Dehydrogenase NdbC in Redox Regulation of Carbon Allocation in Synechocystis

Role of Type 2 NAD(P)H Dehydrogenase NdbC in Redox Regulation of Carbon Allocation in Synechocystis

Cyanobacterial defense mechanisms against foreign DNA transfer and their impact on genetic engineering

Recognition of a pseudo-symmetric RNA tetranucleotide by Csx3, a new member of the CRISPR associated Rossmann fold superfamily

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