|
1
|
Tesfaye A: Revealing the therapeutic uses
of garlic (Allium sativum) and its potential for drug
discovery. Sci World J. 2021:1–7. 2021.PubMed/NCBI View Article : Google Scholar
|
|
2
|
Tsuneyoshi T: BACH1 mediates the
antioxidant properties of aged garlic extract. Exp Ther Med.
19:1500–1503. 2020.PubMed/NCBI View Article : Google Scholar
|
|
3
|
Kanamori Y, Via LD, Macone A, Canettieri
G, Greco A, Toninello A and Agostinelli E: Aged garlic extract and
its constituent, S-allyl-L-cysteine, induce the apoptosis of
neuroblastoma cancer cells due to mitochondrial membrane
depolarization. Exp Ther Med. 19:1511–1521. 2020.PubMed/NCBI View Article : Google Scholar
|
|
4
|
Nakamoto M, Kunimura K, Suzuki JI and
Kodera Y: Antimicrobial properties of hydrophobic compounds in
garlic: Allicin, vinyldithiin, ajoene and diallyl polysulfides. Exp
Ther Med. 19:1550–1553. 2020.PubMed/NCBI View Article : Google Scholar
|
|
5
|
Khounganian RM, Alwakeel A, Albadah A,
Nakshabandi A, Alharbi S and Almslam AS: The antifungal efficacy of
pure garlic, onion, and lemon extracts against Candida
albicans. Cureus. 15(e38637)2023.PubMed/NCBI View Article : Google Scholar
|
|
6
|
Hutchins E, Shaikh K, Kinninger A,
Cherukuri L, Birudaraju D, Mao SS, Nakanishi R, Almeida S,
Jayawardena E, Shekar C, et al: Aged garlic extract reduces left
ventricular myocardial mass in patients with diabetes: A
prospective randomized controlled double-blind study. Exp Ther Med.
19:1468–1471. 2020.PubMed/NCBI View Article : Google Scholar
|
|
7
|
Shaikh K, Kinninger A, Cherukuri L,
Birudaraju D, Nakanishi R, Almeida S, Jayawardena E, Shekar C,
Flores F, Hamal S, et al: Aged garlic extract reduces low
attenuation plaque in coronary arteries of patients with diabetes:
A randomized, double-blind, placebo-controlled study. Exp Ther Med.
19:1457–1461. 2020.PubMed/NCBI View Article : Google Scholar
|
|
8
|
Ohtani M and Nishimura T: The preventive
and therapeutic application of garlic and other plant ingredients
in the treatment of periodontal diseases. Exp Ther Med.
19:1507–1510. 2020.PubMed/NCBI View Article : Google Scholar
|
|
9
|
Mann J, Bernstein Y and Findler M:
Periodontal disease and its prevention, by traditional and new
avenues. Exp Ther Med. 19:1504–1506. 2020.PubMed/NCBI View Article : Google Scholar
|
|
10
|
Gruenwald J, Bongartz U, Bothe G and
Uebelhack R: Effects of aged garlic extract on arterial elasticity
in a placebo-controlled clinical trial using EndoPAT™
technology. Exp Ther Med. 19:1490–1499. 2020.PubMed/NCBI View Article : Google Scholar
|
|
11
|
Matsutomo T: Potential benefits of garlic
and other dietary supplements for the management of hypertension.
Exp Ther Med. 19:1479–1484. 2020.PubMed/NCBI View Article : Google Scholar
|
|
12
|
Ried K: Garlic lowers blood pressure in
hypertensive subjects, improves arterial stiffness and gut
microbiota: A review and meta-analysis. Exp Ther Med. 19:1472–1478.
2020.PubMed/NCBI View Article : Google Scholar
|
|
13
|
Kosuge Y: Neuroprotective mechanisms of
S-allyl-L-cysteine in neurological disease. Exp Ther Med.
19:1565–1569. 2020.PubMed/NCBI View Article : Google Scholar
|
|
14
|
Sripanidkulchai B: Benefits of aged garlic
extract on Alzheimer's disease: Possible mechanisms of action. Exp
Ther Med. 19:1560–1564. 2020.PubMed/NCBI View Article : Google Scholar
|
|
15
|
Rahman K and Lowe GM: Garlic and
cardiovascular disease: A critical review. J Nutr. 136 (Suppl
3):736S–740S. 2006.PubMed/NCBI View Article : Google Scholar
|
|
16
|
Gruhlke MCH, Nicco C, Batteux F and
Slusarenko AJ: The effects of allicin, a reactive sulfur species
from garlic, on a selection of mammalian cell lines. Antioxidants
(Basel). 6(1)2016.PubMed/NCBI View Article : Google Scholar
|
|
17
|
Kita T, Kume N, Minami M, Hayashida K,
Murayama T, Sano H, Moriwaki H, Kataoka H, Nishi E, Horiuchi H, et
al: Role of oxidized LDL in atherosclerosis. Ann N Y Acad Sci.
947:199–206. 2001.PubMed/NCBI View Article : Google Scholar
|
|
18
|
Stoll A and Seebeck E: About alliin, the
genuine mother substance of garlic oil. Helv Chim Acta. 31:189–210.
1948.PubMed/NCBI View Article : Google Scholar : (In German).
|
|
19
|
Cavallito CJ and Bailey JH: Allicin, the
antibacterial principle of Allium sativum I. isolation,
physical properties and antibacterial action. J Am Chem Soc.
66:1950–1951. 1944.
|
|
20
|
Kim YS, Kim KS, Han I, Kim MH, Jung MH and
Park HK: Quantitative and qualitative analysis of the antifungal
activity of allicin alone and in combination with antifungal drugs.
PLoS One. 7(e38242)2012.PubMed/NCBI View Article : Google Scholar
|
|
21
|
Yoshimoto N and Saito K:
S-Alk(en)ylcysteine sulfoxides in the genus Allium: Proposed
biosynthesis, chemical conversion, and bioactivities. J Exp Bot.
70:4123–4137. 2019.PubMed/NCBI View Article : Google Scholar
|
|
22
|
Valentino H, Campbell AC, Schuermann JP,
Sultana N, Nam HG, LeBlanc S, Tanner JJ and Sobrado P: Structure
and function of a flavin-dependent S-monooxygenase from garlic
(Allium sativum). J Biol Chem. 295:11042–11055.
2020.PubMed/NCBI View Article : Google Scholar
|
|
23
|
Borlinghaus J, Albrecht F, Gruhlke MC,
Nwachukwu ID and Slusarenko AJ: Allicin: Chemistry and biological
properties. Molecules. 19:12591–12618. 2014.PubMed/NCBI View Article : Google Scholar
|
|
24
|
Yoshimoto N, Yabe A, Sugino Y, Murakami S,
Sai-Ngam N, Sumi S, Tsuneyoshi T and Saito K: Garlic γ-glutamyl
transpeptidases that catalyze deglutamylation of biosynthetic
intermediate of alliin. Front Plant Sci. 5(758)2014.PubMed/NCBI View Article : Google Scholar
|
|
25
|
Sun X, Zhu S, Li N, Cheng Y, Zhao J, Qiao
X, Lu L, Liu S, Wang Y, Liu C, et al: A chromosome-level genome
assembly of garlic (Allium sativum) provides insights into
genome evolution and allicin biosynthesis. Mol Plant. 13:1328–1339.
2020.PubMed/NCBI View Article : Google Scholar
|
|
26
|
Sayers EW, Cavanaugh M, Clark K, Pruitt
KD, Sherry ST, Yankie L and Karsch-Mizrachi I: GenBank 2023 update.
Nucleic Acids Res. 51 (D1):D141–D144. 2023.PubMed/NCBI View Article : Google Scholar
|
|
27
|
Stein L: Generic feature format version 3
(GFF3). GitHub, 2020.
|
|
28
|
Camacho C, Coulouris G, Avagyan V, Ma N,
Papadopoulos J, Bealer K and Madden TL: BLAST+: architecture and
applications. BMC Bioinformatics. 10(421)2009.PubMed/NCBI View Article : Google Scholar
|
|
29
|
Slater GS and Birney E: Automated
generation of heuristics for biological sequence comparison. BMC
Bioinformatics. 6(31)2005.PubMed/NCBI View Article : Google Scholar
|
|
30
|
Thorvaldsdóttir H, Robinson JT and Mesirov
JP: Integrative genomics viewer (IGV): High-performance genomics
data visualization and exploration. Brief Bioinform. 14:178–192.
2013.PubMed/NCBI View Article : Google Scholar
|
|
31
|
Brown TA: Chapter 10 synthesis and
processing of RNA. In: Genomes. 2nd edition Oxford: Wiley-Liss,
2002.
|
|
32
|
Dainat J: AGAT: Another Gff Analysis
Toolkit to handle annotations in any GTF/GFF format (version
v0.4.0). Zenodo, 2020.
|
|
33
|
Needleman SB and Wunsch CD: A general
method applicable to the search for similarities in the amino acid
sequence of two proteins. J Mol Biol. 48:443–453. 1970.PubMed/NCBI View Article : Google Scholar
|
|
34
|
Sievers F, Wilm A, Dineen D, Gibson TJ,
Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, et al:
Fast, scalable generation of high-quality protein multiple sequence
alignments using Clustal Omega. Mol Syst Biol.
7(539)2011.PubMed/NCBI View Article : Google Scholar
|
|
35
|
Eddy SR: HMMER development team: HMMER
user's guide. Biological sequence analysis using profile hidden
Markov models, version 3.3.2. http://hmmer.org/. Accessed Nov 2020, 2020.
|
|
36
|
Kanost MR, Arrese EL, Cao X, Chen YR,
Chellapilla S, Goldsmith MR, Grosse-Wilde E, Heckel DG, Herndon N,
Jiang H, et al: Multifaceted biological insights from a draft
genome sequence of the tobacco hornworm moth, Manduca sexta. Insect
Biochem Mol Biol. 76:118–147. 2016.PubMed/NCBI View Article : Google Scholar
|
|
37
|
UniProt Consortium: UniProt: The universal
protein knowledgebase in 2023. Nucleic Acids Res. 51
(D1):D523–D531. 2023.PubMed/NCBI View Article : Google Scholar
|
|
38
|
Teufel F, Almagro Armenteros JJ, Johansen
AR, Gíslason MH, Pihl SI, Tsirigos KD, Winther O, Brunak S, von
Heijne G and Nielsen H: SignalP 6.0 predicts all five types of
signal peptides using protein language models. Nat Biotechnol.
40:1023–1025. 2022.PubMed/NCBI View Article : Google Scholar
|
|
39
|
Hallgren J, Tsirigos KD, Damgaard Pedersen
M, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A and
Winther O: DeepTMHMM predicts alpha and beta transmembrane proteins
using deep neural networks. bioRxiv: doi: https://doi.org/10.1101/2022.04.08.487609.
|
|
40
|
Katz K, Shutov O, Lapoint R, Kimelman M,
Brister JR and O'Sullivan C: The sequence read archive: A decade
more of explosive growth. Nucleic Acids Res. 50 (D1):D387–D390.
2022.PubMed/NCBI View Article : Google Scholar
|
|
41
|
Burgin J, Ahamed A, Cummins C, Devraj R,
Gueye K, Gupta D, Gupta V, Haseeb M, Ihsan M, Ivanov E, et al: The
European nucleotide archive in 2022. Nucleic Acids Res. 51
(D1):D121–D125. 2023.PubMed/NCBI View Article : Google Scholar
|
|
42
|
Rice P, Longden I and Bleasby A: EMBOSS:
The European molecular biology open software suite. Trends Genet.
16:276–277. 2000.PubMed/NCBI View Article : Google Scholar
|
|
43
|
Jumper J, Evans R, Pritzel A, Green T,
Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Žídek A,
Potapenko A, et al: Highly accurate protein structure prediction
with AlphaFold. Nature. 596:583–589. 2021.PubMed/NCBI View Article : Google Scholar
|
|
44
|
Varadi M, Anyango S, Deshpande M, Nair S,
Natassia C, Yordanova G, Yuan D, Stroe O, Wood G, Laydon A, et al:
AlphaFold protein structure database: Massively expanding the
structural coverage of protein-sequence space with high-accuracy
models. Nucleic Acids Res. 50 (D1):D439–D444. 2022.PubMed/NCBI View Article : Google Scholar
|
|
45
|
Mirdita M, Schütze K, Moriwaki Y, Heo L,
Ovchinnikov S and Steinegger M: ColabFold: Making protein folding
accessible to all. Nat Methods. 19:679–682. 2022.PubMed/NCBI View Article : Google Scholar
|
|
46
|
Waterhouse A, Bertoni M, Bienert S, Studer
G, Tauriello G, Gumienny R, Heer FT, de Beer TAP, Rempfer C,
Bordoli L, et al: SWISS-MODEL: Homology modelling of protein
structures and complexes. Nucleic Acids Res. 46 (W1):W296–W303.
2018.PubMed/NCBI View Article : Google Scholar
|
|
47
|
Berman HM, Westbrook J, Feng Z, Gilliland
G, Bhat TN, Weissig H, Shindyalov IN and Bourne PE: The protein
data bank. Nucleic Acids Res. 28:235–242. 2000.PubMed/NCBI View Article : Google Scholar
|
|
48
|
Edgar RC: MUSCLE: Multiple sequence
alignment with high accuracy and high throughput. Nucleic Acids
Res. 32:1792–1797. 2004.PubMed/NCBI View Article : Google Scholar
|
|
49
|
Waterhouse AM, Procter JB, Martin DMA,
Clamp M and Barton GJ: Jalview version 2-a multiple sequence
alignment editor and analysis workbench. Bioinformatics.
25:1189–1191. 2009.PubMed/NCBI View Article : Google Scholar
|
|
50
|
Archie J, Day WH, Maddison W, Meacham C,
Rohlf FJ, Swofford D and Felsenstein J: The Newick tree format.
http://evolution.genetics.washington.edu/phylip/newicktree.html.
|
|
51
|
Huson DH and Scornavacca C: Dendroscope 3:
An interactive tool for rooted phylogenetic trees and networks.
Syst Biol. 61:1061–1067. 2012.PubMed/NCBI View Article : Google Scholar
|
|
52
|
Schrödinger LLC: The PyMOL molecular
graphics system. PyMOL, 2023.
|
|
53
|
Strauss BS: Frameshift mutation,
microsatellites and mismatch repair. Mutat Res. 437:195–203.
1999.PubMed/NCBI View Article : Google Scholar
|
|
54
|
Treangen TJ and Salzberg SL: Repetitive
DNA and next-generation sequencing: Computational challenges and
solutions. Nat Rev Genet. 13:36–46. 2011.PubMed/NCBI View Article : Google Scholar
|
|
55
|
West MB, Wickham S, Parks EE, Sherry DM
and Hanigan MH: Human GGT2 does not autocleave into a functional
enzyme: A cautionary tale for interpretation of microarray data on
redox signaling. Antioxid Redox Signal. 19:1877–1888.
2013.PubMed/NCBI View Article : Google Scholar
|
|
56
|
Bradley K, Rieger MA and Collins GG:
Classification of Australian garlic cultivars by DNA
fingerprinting. Aust J Exp Agric. 36:613–618. 1996.
|
|
57
|
González RE, Soto VC, Sance MM, Camargo AB
and Galmarini CR: Variability of solids, organosulfur compounds,
pungency and health-enhancing traits in garlic (Allium
sativum L.) cultivars belonging to different ecophysiological
groups. J Agric Food Chem. 57:10282–10288. 2009.PubMed/NCBI View Article : Google Scholar
|
|
58
|
Dalbey RE and Robinson C: Protein
translocation into and across the bacterial plasma membrane and the
plant thylakoid membrane. Trends Biochem Sci. 24:17–22.
1999.PubMed/NCBI View Article : Google Scholar
|
|
59
|
Driessen AJ, Manting EH and van der Does
C: The structural basis of protein targeting and translocation in
bacteria. Nat Struct Biol. 8:492–498. 2001.PubMed/NCBI View
Article : Google Scholar
|
|
60
|
Tjalsma H, Bolhuis A, Jongbloed JD, Bron S
and van Dijl JM: Signal peptide-dependent protein transport in
Bacillus subtilis: A genome-based survey of the secretome.
Microbiol Mol Biol Rev. 64:515–547. 2000.PubMed/NCBI View Article : Google Scholar
|
|
61
|
Briggs MS, Cornell DG, Dluhy RA and
Gierasch LM: Conformations of signal peptides induced by lipids
suggest initial steps in protein export. Science. 233:206–208.
1986.PubMed/NCBI View Article : Google Scholar
|
|
62
|
Suzuki H, Kumagai H and Tochikura T:
gamma-Glutamyltranspeptidase from Escherichia coli K-12: Formation
and localization. J Bacteriol. 168:1332–1335. 1986.PubMed/NCBI View Article : Google Scholar
|
|
63
|
Tate SS and Meister A: gamma-Glutamyl
transpeptidase: Catalytic, structural and functional aspects. Mol
Cell Biochem. 39:357–368. 1981.PubMed/NCBI View Article : Google Scholar
|
|
64
|
Thul PJ, Åkesson L, Wiking M, Mahdessian
D, Geladaki A, Ait Blal H, Alm T, Asplund A, Björk L, Breckels LM,
et al: A subcellular map of the human proteome. Science.
356(eaal3321)2017.PubMed/NCBI View Article : Google Scholar
|
|
65
|
Koonin E and Galperin M: Chapter 2
evolutionary concept in genetics and genomics. In:
Sequence-evolution-function: Computational approaches in
comparative genomics. Kluwer Academic, Boston, 2003.
|
|
66
|
Jones MG, Hughes J, Tregova A, Milne J,
Tomsett AB and Collin HA: Biosynthesis of the flavour precursors of
onion and garlic. J Exp Bot. 55:1903–1918. 2004.PubMed/NCBI View Article : Google Scholar
|
|
67
|
Penninckx MJ and Jaspers CJ: Molecular and
kinetic properties of purified γ-glutamyl transpeptidase from yeast
(Saccharomyces cerevisiae). Phytochemistry. 24:1913–1918.
1985.
|
|
68
|
Storozhenko S, Belles-Boix E, Babiychuk E,
Hérouart D, Davey MW, Slooten L, Van Montagu M, Inzé D and Kushnir
S: Gamma-glutamyl transpeptidase in transgenic tobacco plants.
Cellular localization, processing, and biochemical properties.
Plant Physiol. 128:1109–1119. 2002.PubMed/NCBI View Article : Google Scholar
|
|
69
|
Lancaster JE and Shaw ML: Characterization
of purified γ-glutamyl transpeptidase in onions: Evidence for in
vivo role as a peptidase. Phytochemistry. 36:1351–1358. 1994.
|
|
70
|
Nakano Y, Okawa S, Yamauchi T, Koizumi Y
and Sekiya J: Purification and properties of soluble and bound
gamma-glutamyltransferases from radish cotyledon. Biosci Biotechnol
Biochem. 70:369–376. 2006.PubMed/NCBI View Article : Google Scholar
|
|
71
|
Ikeda Y, Fujii J, Taniguchi N and Meister
A: Human gamma-glutamyl transpeptidase mutants involving conserved
aspartate residues and the unique cysteine residue of the light
subunit. J Biol Chem. 270:12471–12475. 1995.PubMed/NCBI
|
|
72
|
Okada T, Suzuki H, Wada K, Kumagai H and
Fukuyama K: Crystal structures of gamma-glutamyltranspeptidase from
Escherichia coli, a key enzyme in glutathione metabolism, and its
reaction intermediate. Proc Natl Acad Sci USA. 103:6471–6476.
2006.PubMed/NCBI View Article : Google Scholar
|
|
73
|
Grzam A, Martin MN, Hell R and Meyer AJ:
gamma-Glutamyl transpeptidase GGT4 initiates vacuolar degradation
of glutathione S-conjugates in Arabidopsis. FEBS Lett.
581:3131–3138. 2007.PubMed/NCBI View Article : Google Scholar
|
|
74
|
Ohkama-Ohtsu N, Radwan S, Peterson A, Zhao
P, Badr AF, Xiang C and Oliver DJ: Characterization of the
extracellular gamma-glutamyl transpeptidases, GGT1 and GGT2, in
Arabidopsis. Plant J. 49:865–877. 2007.PubMed/NCBI View Article : Google Scholar
|
|
75
|
Ohkama-Ohtsu N, Zhao P, Xiang C and Oliver
DJ: Glutathione conjugates in the vacuole are degraded by
gamma-glutamyl transpeptidase GGT3 in Arabidopsis. Plant J.
49:878–888. 2007.PubMed/NCBI View Article : Google Scholar
|
|
76
|
Martin MN, Saladores PH, Lambert E, Hudson
AO and Leustek T: Localization of members of the gamma-glutamyl
transpeptidase family identifies sites of glutathione and
glutathione S-conjugate hydrolysis. Plant Physiol. 144:1715–1732.
2007.PubMed/NCBI View Article : Google Scholar
|
|
77
|
Shaw ML, Pither-Joyce MD and McCallum JA:
Purification and cloning of a gamma-glutamyl transpeptidase from
onion (Allium cepa). Phytochemistry. 66:515–522.
2005.PubMed/NCBI View Article : Google Scholar
|
