2020
DOI: 10.1186/s12915-020-00885-2
|View full text |Cite
|
Sign up to set email alerts
|

Modified base-binding EVE and DCD domains: striking diversity of genomic contexts in prokaryotes and predicted involvement in a variety of cellular processes

Abstract: Background DNA and RNA of all cellular life forms and many viruses contain an expansive repertoire of modified bases. The modified bases play diverse biological roles that include both regulation of transcription and translation, and protection against restriction endonucleases and antibiotics. Modified bases are often recognized by dedicated protein domains. However, the elaborate networks of interactions and processes mediated by modified bases are far from being completely understood. … Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
2
2
1

Citation Types

2
13
0

Year Published

2021
2021
2024
2024

Publication Types

Select...
4
2

Relationship

1
5

Authors

Journals

citations
Cited by 10 publications
(15 citation statements)
references
References 157 publications
2
13
0
Order By: Relevance
“…The pollen-pistil interaction 2 gene (POP2), involved in fertilization regulation in angiosperms (Renault et al, 2011), was acquired from bacteria during episode 1 (Figure 4E). EVE domain-containing proteins (or thymocyte nuclear-like proteins), widely distributed in streptophytes and bacteria, are thought to be functionally related to programmed cell death (Bell et al, 2020). Consistent with an earlier finding (Bell et al, 2020), our data show that plant EVE domaincontaining protein genes are derived from bacteria (Supplemental Figure 14).…”
Section: Growth and Developmentsupporting
confidence: 90%
See 1 more Smart Citation
“…The pollen-pistil interaction 2 gene (POP2), involved in fertilization regulation in angiosperms (Renault et al, 2011), was acquired from bacteria during episode 1 (Figure 4E). EVE domain-containing proteins (or thymocyte nuclear-like proteins), widely distributed in streptophytes and bacteria, are thought to be functionally related to programmed cell death (Bell et al, 2020). Consistent with an earlier finding (Bell et al, 2020), our data show that plant EVE domaincontaining protein genes are derived from bacteria (Supplemental Figure 14).…”
Section: Growth and Developmentsupporting
confidence: 90%
“…EVE domain-containing proteins (or thymocyte nuclear-like proteins), widely distributed in streptophytes and bacteria, are thought to be functionally related to programmed cell death (Bell et al, 2020). Consistent with an earlier finding (Bell et al, 2020), our data show that plant EVE domaincontaining protein genes are derived from bacteria (Supplemental Figure 14). At least three acquired genes have been shown experimentally to modulate vascular development (Jun et al, 2002;Yang et al, 2015;Ribeiro et al, 2020) (Supplemental Table 5).…”
Section: Growth and Developmentsupporting
confidence: 90%
“…In contrast to Type II and Type III CnuB homologs, which contain only coiled-coils fused at their N-termini (Figure 6), cold-shock domain (CSD)-like OB-folds are usually fused at the N-termini of Type I CoCoNuT CnuB/McrB proteins, in addition to the coiled-coils (except for the majority of Type I-B, where the coiled-coils are encoded separately) (Figure 5, Supplementary Table S1) (Amir et al, 2018). Often, in Type I-B and I-C, but not Type I-A, a YTH-like domain, a member of the modified base-binding EVE superfamily, is present in CnuB as well, between the CSD and coiled-coil, or in Type I-B, between the CSD and the GTPase domain (Figure 5, Supplementary Table S1) (Bell et al, 2020, Hazra et al, 2019, Liao et al, 2018).…”
Section: Resultsmentioning
confidence: 99%
“…In recent years, systematic searches for defense systems in prokaryotes, primarily by analysis of defense islands, revealed enormous, previously unsuspected diversity of such systems that function through a remarkable variety of molecular mechanisms. In this work, we (Bell et al, 2020). All alignments were clustered, and each sub-alignment or individual query sequence was used to produce a position-specific scoring matrix (PSSM).…”
Section: Discussionmentioning
confidence: 99%
“…More recently, the EVE protein domain in the PUA superfamily has been found in fusion with the HNH nuclease domain to provide restriction of hm5C/m5C-modified DNA ( Lutz et al, 2019 ). EVE domain can be fused with PD-D/E xK nuclease and other nuclease domains such as Pin nuclease, PLD nuclease, and GIY-YIG family nucleases ( Bell et al, 2020 ). SauUSI is another example of Type IV REases with PLD nuclease-DNA helicase (ATPase)-Sra domain fusion that restricts hm5C/m5C modified DNA ( Xu et al, 2011 ; Tumuluri et al, 2021 ).…”
Section: Discussionmentioning
confidence: 99%