1
|
Reddy K, Renuka N, Kumari S, Bux F. Algae-mediated processes for the treatment of antiretroviral drugs in wastewater: Prospects and challenges. CHEMOSPHERE 2021; 280:130674. [PMID: 34162077 DOI: 10.1016/j.chemosphere.2021.130674] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 06/13/2023]
Abstract
The prevalence of pharmaceuticals (PCs), especially antiretroviral (ARV) drugs in various aquatic ecosystems has been expansively reported, wherein wastewater treatment plants (WWTPs) are identified as the primary point source. Consequently, the occurrence, ecotoxicity and treatment of ARV drugs in WWTPs have drawn much attention in recent years. Numerous studies have shown that the widely employed activated sludge-based WWTPs are incapable of removing ARV drugs efficiently from wastewater. Recently, algae-based wastewater treatment processes have shown promising results in PCs removal from wastewater, either completely or partially, through different processes such as biosorption, bioaccumulation, and intra-/inter-cellular degradation. Algal species have also shown to tolerate high concentrations of ARV drugs than the reported concentrations in the environmental matrices. In this review, emphasis has been given on discussing the current status of the occurrence of ARV drugs in the aquatic environment and WWTPs. Besides, the current trends and future perspectives of PCs removal by algae are critically reviewed and discussed. The potential pathways and mechanisms of ARV drugs removal by algae have also been discussed.
Collapse
Affiliation(s)
- Karen Reddy
- Institute for Water and Wastewater Technology, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Nirmal Renuka
- Institute for Water and Wastewater Technology, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa.
| |
Collapse
|
2
|
Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages. ISME JOURNAL 2015; 10:1134-46. [PMID: 26613339 PMCID: PMC5029228 DOI: 10.1038/ismej.2015.192] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 08/27/2015] [Accepted: 09/22/2015] [Indexed: 11/18/2022]
Abstract
Genes encoding reverse transcriptases (RTs) are found in most eukaryotes, often
as a component of retrotransposons, as well as in retroviruses and in
prokaryotic retroelements. We investigated the abundance, classification and
transcriptional status of RTs based on Tara Oceans marine metagenomes
and metatranscriptomes encompassing a wide organism size range. Our analyses
revealed that RTs predominate large-size fraction metagenomes
(>5 μm), where they reached a maximum of 13.5% of the total
gene abundance. Metagenomic RTs were widely distributed across the phylogeny of
known RTs, but many belonged to previously uncharacterized clades.
Metatranscriptomic RTs showed distinct abundance patterns across samples
compared with metagenomic RTs. The relative abundances of viral and bacterial
RTs among identified RT sequences were higher in metatranscriptomes than in
metagenomes and these sequences were detected in all metatranscriptome size
fractions. Overall, these observations suggest an active proliferation of
various RT-assisted elements, which could be involved in genome evolution or
adaptive processes of plankton assemblage.
Collapse
|
3
|
Luo S, Mach J, Abramson B, Ramirez R, Schurr R, Barone P, Copenhaver G, Folkerts O. The cotton centromere contains a Ty3-gypsy-like LTR retroelement. PLoS One 2012; 7:e35261. [PMID: 22536361 DOI: 10.1371/journal.pone.0035261] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 03/13/2012] [Indexed: 01/16/2023] Open
Abstract
The centromere is a repeat-rich structure essential for chromosome segregation; with the long-term aim of understanding centromere structure and function, we set out to identify cotton centromere sequences. To isolate centromere-associated sequences from cotton, (Gossypium hirsutum) we surveyed tandem and dispersed repetitive DNA in the genus. Centromere-associated elements in other plants include tandem repeats and, in some cases, centromere-specific retroelements. Examination of cotton genomic survey sequences for tandem repeats yielded sequences that did not localize to the centromere. However, among the repetitive sequences we also identified a gypsy-like LTR retrotransposon (Centromere Retroelement Gossypium, CRG) that localizes to the centromere region of all chromosomes in domestic upland cotton, Gossypium hirsutum, the major commercially grown cotton. The location of the functional centromere was confirmed by immunostaining with antiserum to the centromere-specific histone CENH3, which co-localizes with CRG hybridization on metaphase mitotic chromosomes. G. hirsutum is an allotetraploid composed of A and D genomes and CRG is also present in the centromere regions of other AD cotton species. Furthermore, FISH and genomic dot blot hybridization revealed that CRG is found in D-genome diploid cotton species, but not in A-genome diploid species, indicating that this retroelement may have invaded the A-genome centromeres during allopolyploid formation and amplified during evolutionary history. CRG is also found in other diploid Gossypium species, including B and E2 genome species, but not in the C, E1, F, and G genome species tested. Isolation of this centromere-specific retrotransposon from Gossypium provides a probe for further understanding of centromere structure, and a tool for future engineering of centromere mini-chromosomes in this important crop species.
Collapse
Affiliation(s)
- Song Luo
- Chromatin, Inc., Chicago, Illinois, United States of America
| | | | | | | | | | | | | | | |
Collapse
|
4
|
Villarreal LP. The source of self: genetic parasites and the origin of adaptive immunity. Ann N Y Acad Sci 2009; 1178:194-232. [PMID: 19845639 DOI: 10.1111/j.1749-6632.2009.05020.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Stable colonization of the host by viruses (genetic parasites) can alter the systems of host identity and provide immunity against related viruses. To attain the needed stability, some viruses of prokaryotes (P1 phage) use a strategy called an addiction module. The linked protective and destructive gene functions of an addiction module insures both virus persistence but will also destroy cells that interrupt this module and thereby prevent infection by competitors. Previously, I have generalized this concept to also include persistent and lytic states of virus infection, which can be considered as a virus addiction module. Such states often involve defective viruses. In this report, I examine the origin of the adaptive immune system from the perspective of a virus addiction module. The likely role of both endogenous and exogenous retroviruses, DNA viruses, and their defective elements is considered in the origin of all the basal components of adaptive immunity (T-cell receptor, RAG-mediated gene rearrangement, clonal lymphocyte proliferation, antigen surface presentation, apoptosis, and education of immune cells). It is concluded that colonization by viruses and their defectives provides a more coherent explanation for the origin of adaptive immunity.
Collapse
Affiliation(s)
- Luis P Villarreal
- Center for Virus Research, Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA.
| |
Collapse
|
5
|
Donaher N, Tanifuji G, Onodera NT, Malfatti SA, Chain PSG, Hara Y, Archibald JM. The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate. Genome Biol Evol 2009; 1:439-48. [PMID: 20333213 PMCID: PMC2839278 DOI: 10.1093/gbe/evp047] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2009] [Indexed: 12/23/2022] Open
Abstract
The cryptomonads are a group of unicellular algae that acquired photosynthesis through the engulfment of a red algal cell, a process called secondary endosymbiosis. Here, we present the complete plastid genome sequence of the secondarily nonphotosynthetic species Cryptomonas paramecium CCAP977/2a. The ∼78 kilobase pair (Kbp) C. paramecium genome contains 82 predicted protein genes, 29 transfer RNA genes, and a single pseudogene (atpF). The C. paramecium plastid genome is approximately 50 Kbp smaller than those of the photosynthetic cryptomonads Guillardia theta and Rhodomonas salina; 71 genes present in the G. theta and/or R. salina plastid genomes are missing in C. paramecium. The pet, psa, and psb photosynthetic gene families are almost entirely absent. Interestingly, the ribosomal RNA operon, present as inverted repeats in most plastid genomes (including G. theta and R. salina), exists as a single copy in C. paramecium. The G + C content (38%) is higher in C. paramecium than in other cryptomonad plastid genomes, and C. paramecium plastid genes are characterized by significantly different codon usage patterns and increased evolutionary rates. The content and structure of the C. paramecium plastid genome provides insight into the changes associated with recent loss of photosynthesis in a predominantly photosynthetic group of algae and reveals features shared with the plastid genomes of other secondarily nonphotosynthetic eukaryotes.
Collapse
Affiliation(s)
- Natalie Donaher
- Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | | | | | | | | | | |
Collapse
|
6
|
Peddigari S, Zhang W, Takechi K, Takano H, Takio S. Two different clades of copia-like retrotransposons in the red alga, Porphyra yezoensis. Gene 2008; 424:153-8. [PMID: 18708130 DOI: 10.1016/j.gene.2008.07.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2007] [Revised: 07/16/2008] [Accepted: 07/21/2008] [Indexed: 12/11/2022]
Abstract
A copia-like retrotransposon referred to as PyRE1G1 was isolated from the genome of the red alga Porphyra yezoensis. PyRE1G1 is 4807 bp in length, with 204 bp long terminal repeats (LTRs) at both ends. PyRE1G1 has an open reading frame of 1401 residues encoding gag, protease, integrase, reverse transcriptase (RT), and RNase H. From the order of gene arrangement of proteins, PyRE1G1 appears to be a copia-like retrotransposon. Genomic Southern blot analysis suggests that PyRE1G1 consists of a small gene family. From the phylogenetic tree of RT sequences, PyRE1G1 is grouped in the clade of usual copia elements and distinct from the previously isolated red algal copia-like gene PyRE10G in that the latter is closely related to a new clade of aquatic animal-specific copia-like retrotransposons.
Collapse
Affiliation(s)
- Suresh Peddigari
- Graduate School of Science and Technology, Kumamoto University, Kurokami, Kumamoto 860-8555, Japan
| | | | | | | | | |
Collapse
|
7
|
Carr M, Nelson M, Leadbeater BSC, Baldauf SL. Three families of LTR retrotransposons are present in the genome of the choanoflagellate Monosiga brevicollis. Protist 2008; 159:579-90. [PMID: 18621583 DOI: 10.1016/j.protis.2008.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Accepted: 05/01/2008] [Indexed: 11/29/2022]
Abstract
The choanoflagellates are a ubiquitous group of nanoflagellates and the sister group of Metazoa. Examination of the initial draft version of the first choanoflagellate genome, that of Monosiga brevicollis, reveals the presence of three novel families of long terminal repeat (LTR) retrotransposons and an apparent absence of non-LTR retrotransposons and transposons. One of the newly discovered LTR families falls in the chromovirus clade of the Ty3/gypsy group while the other two families are closely related members of the Ty1/copia group. Examination of EST sequences and nucleotide analyses show that all three families are transcriptionally active and potentially functional within the genome of M. brevicollis.
Collapse
Affiliation(s)
- Martin Carr
- Department of Biology, University of York, Heslington, York YO10 5YW, UK
| | | | | | | |
Collapse
|
8
|
Abstract
Cryptophytes are unicellular eukaryotic algae that acquired photosynthesis secondarily through the uptake and retention of a red-algal endosymbiont. The plastid genome of the cryptophyte Rhodomonas salina CCMP1319 was recently sequenced and found to contain a genetic element similar to a group II intron. Here, we explore the distribution, structure and function of group II introns in the plastid genomes of distantly and closely related cryptophytes. The predicted secondary structures of six introns contained in three different genes were examined and found to be generally similar to group II introns but unusually large in size (including the largest known noncoding intron). Phylogenetic analysis suggests that the cryptophyte group II introns were acquired via lateral gene transfer (LGT) from a euglenid-like species. Unexpectedly, the six introns occupy five distinct genomic locations, suggesting multiple LGT events or recent transposition (or both). Combined with structural considerations, RT–PCR experiments suggest that the transferred introns are degenerate ‘twintrons’ (i.e. nested group II/group III introns) in which the internal intron has lost its splicing capability, resulting in an amalgamation with the outer intron.
Collapse
Affiliation(s)
- Hameed Khan
- Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
| | | |
Collapse
|